3o1s - Revision history

OCA at 09:25, 6 September 2023

2023-09-06T09:25:44Z

←Older revision		Revision as of 09:25, 6 September 2023
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	<StructureSection load='3o1s' size='340' side='right'caption='[[3o1s]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='3o1s' size='340' side='right'caption='[[3o1s]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3o1s]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O1S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O1S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3o1s]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O1S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O1S FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>~~, ~~<scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.58Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=2YR:2-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>2YR</scene>, <scene name='pdbligand=MDQ:2-DEOXY-3-(OXIDOMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>MDQ</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2YR:2-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>2YR</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MDQ:2-DEOXY-3-(OXIDOMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>MDQ</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[3o1m\|3o1m]], [[3o1o\|3o1o]], [[3o1p\|3o1p]], [[3o1r\|3o1r]], [[3o1t\|3o1t]], [[3o1u\|3o1u]], [[3o1v\|3o1v]]~~</~~div~~>~~</td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alkB, aidD, b2212, JW2200 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3o1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o1s OCA], [https://pdbe.org/3o1s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o1s RCSB], [https://www.ebi.ac.uk/pdbsum/3o1s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o1s ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3o1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o1s OCA], [https://pdbe.org/3o1s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o1s RCSB], [https://www.ebi.ac.uk/pdbsum/3o1s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o1s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ALKB_ECOLI ALKB_ECOLI]] Dioxygenase that repairs alkylated DNA and RNA containing 3-methylcytosine or 1-methyladenine by oxidative demethylation. Has highest activity towards 3-methylcytosine. Has lower activity towards alkylated DNA containing ethenoadenine, and no detectable activity towards 1-methylguanine or 3-methylthymine. Accepts double-stranded and single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron. Provides extensive resistance to alkylating agents such as MMS and DMS (SN2 agents), but not to MMNG and MNU (SN1 agents).<ref>PMID:12226668</ref> <ref>PMID:12594517</ref> <ref>PMID:16482161</ref> <ref>PMID:19706517</ref> <ref>PMID:21068844</ref> <ref>PMID:20084272</ref>	+	[https://www.uniprot.org/uniprot/ALKB_ECOLI ALKB_ECOLI] Dioxygenase that repairs alkylated DNA and RNA containing 3-methylcytosine or 1-methyladenine by oxidative demethylation. Has highest activity towards 3-methylcytosine. Has lower activity towards alkylated DNA containing ethenoadenine, and no detectable activity towards 1-methylguanine or 3-methylthymine. Accepts double-stranded and single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron. Provides extensive resistance to alkylating agents such as MMS and DMS (SN2 agents), but not to MMNG and MNU (SN1 agents).<ref>PMID:12226668</ref> <ref>PMID:12594517</ref> <ref>PMID:16482161</ref> <ref>PMID:19706517</ref> <ref>PMID:21068844</ref> <ref>PMID:20084272</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cui, Q]]	+	[[Category: Cui Q]]
-	[[Category: Dai, Q]]	+	[[Category: Dai Q]]
-	[[Category: He, C]]	+	[[Category: He C]]
-	[[Category: Hou, G]]	+	[[Category: Hou G]]
-	[[Category: Jia, G]]	+	[[Category: Jia G]]
-	[[Category: Jian, X]]	+	[[Category: Jian X]]
-	[[Category: Yang, C G]]	+	[[Category: Yang C-G]]
-	[[Category: Yi, C]]	+	[[Category: Yi C]]
-	[[Category: Zhang, W]]	+	[[Category: Zhang W]]
-	[[Category: Zheng, G]]	+	[[Category: Zheng G]]
-	~~[[Category: Demethylase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:13, 12 May 2022

2022-05-12T07:13:39Z

←Older revision		Revision as of 07:13, 12 May 2022
Line 1:		Line 1:

	==Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase==		==Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase==
-	<StructureSection load='3o1s' size='340' side='right' caption='[[3o1s]], [[Resolution\|resolution]] 1.58Å' scene=''>	+	<StructureSection load='3o1s' size='340' side='right'caption='[[3o1s]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3o1s]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O1S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3O1S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3o1s]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O1S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O1S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2YR:2-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>2YR</scene>, <scene name='pdbligand=MDQ:2-DEOXY-3-(OXIDOMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>MDQ</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2YR:2-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>2YR</scene>, <scene name='pdbligand=MDQ:2-DEOXY-3-(OXIDOMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>MDQ</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3o1m\|3o1m]], [[3o1o\|3o1o]], [[3o1p\|3o1p]], [[3o1r\|3o1r]], [[3o1t\|3o1t]], [[3o1u\|3o1u]], [[3o1v\|3o1v]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3o1m\|3o1m]], [[3o1o\|3o1o]], [[3o1p\|3o1p]], [[3o1r\|3o1r]], [[3o1t\|3o1t]], [[3o1u\|3o1u]], [[3o1v\|3o1v]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alkB, aidD, b2212, JW2200 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alkB, aidD, b2212, JW2200 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3o1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o1s OCA], [~~http~~://pdbe.org/3o1s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3o1s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3o1s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3o1s ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3o1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o1s OCA], [https://pdbe.org/3o1s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o1s RCSB], [https://www.ebi.ac.uk/pdbsum/3o1s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o1s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ALKB_ECOLI ALKB_ECOLI]] Dioxygenase that repairs alkylated DNA and RNA containing 3-methylcytosine or 1-methyladenine by oxidative demethylation. Has highest activity towards 3-methylcytosine. Has lower activity towards alkylated DNA containing ethenoadenine, and no detectable activity towards 1-methylguanine or 3-methylthymine. Accepts double-stranded and single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron. Provides extensive resistance to alkylating agents such as MMS and DMS (SN2 agents), but not to MMNG and MNU (SN1 agents).<ref>PMID:12226668</ref> <ref>PMID:12594517</ref> <ref>PMID:16482161</ref> <ref>PMID:19706517</ref> <ref>PMID:21068844</ref> <ref>PMID:20084272</ref>	+	[[https://www.uniprot.org/uniprot/ALKB_ECOLI ALKB_ECOLI]] Dioxygenase that repairs alkylated DNA and RNA containing 3-methylcytosine or 1-methyladenine by oxidative demethylation. Has highest activity towards 3-methylcytosine. Has lower activity towards alkylated DNA containing ethenoadenine, and no detectable activity towards 1-methylguanine or 3-methylthymine. Accepts double-stranded and single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron. Provides extensive resistance to alkylating agents such as MMS and DMS (SN2 agents), but not to MMNG and MNU (SN1 agents).<ref>PMID:12226668</ref> <ref>PMID:12594517</ref> <ref>PMID:16482161</ref> <ref>PMID:19706517</ref> <ref>PMID:21068844</ref> <ref>PMID:20084272</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:

	==See Also==		==See Also==
-	*[[Dioxygenase\|Dioxygenase]]	+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Cui, Q]]		[[Category: Cui, Q]]
	[[Category: Dai, Q]]		[[Category: Dai, Q]]

OCA at 20:36, 5 August 2016

2016-08-05T20:36:32Z

←Older revision		Revision as of 20:36, 5 August 2016
Line 1:		Line 1:
		+
	==Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase==		==Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase==
	<StructureSection load='3o1s' size='340' side='right' caption='[[3o1s]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='3o1s' size='340' side='right' caption='[[3o1s]], [[Resolution\|resolution]] 1.58Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3o1m\|3o1m]], [[3o1o\|3o1o]], [[3o1p\|3o1p]], [[3o1r\|3o1r]], [[3o1t\|3o1t]], [[3o1u\|3o1u]], [[3o1v\|3o1v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3o1m\|3o1m]], [[3o1o\|3o1o]], [[3o1p\|3o1p]], [[3o1r\|3o1r]], [[3o1t\|3o1t]], [[3o1u\|3o1u]], [[3o1v\|3o1v]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alkB, aidD, b2212, JW2200 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alkB, aidD, b2212, JW2200 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3o1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o1s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3o1s RCSB], [http://www.ebi.ac.uk/pdbsum/3o1s PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3o1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o1s OCA], [http://pdbe.org/3o1s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3o1s RCSB], [http://www.ebi.ac.uk/pdbsum/3o1s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3o1s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3o1s" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase\|Dioxygenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:42, 25 December 2014

2014-12-25T21:42:39Z

←Older revision		Revision as of 21:42, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3o1s]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O1S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3O1S FirstGlance]. <br>		<table><tr><td colspan='2'>[[3o1s]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O1S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3O1S FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2YR:2-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>2YR</scene>, <scene name='pdbligand=MDQ:2-DEOXY-3-(OXIDOMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>MDQ</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2YR:2-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>2YR</scene>, <scene name='pdbligand=MDQ:2-DEOXY-3-(OXIDOMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>MDQ</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3o1m\|3o1m]], [[3o1o\|3o1o]], [[3o1p\|3o1p]], [[3o1r\|3o1r]], [[3o1t\|3o1t]], [[3o1u\|3o1u]], [[3o1v\|3o1v]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3o1m\|3o1m]], [[3o1o\|3o1o]], [[3o1p\|3o1p]], [[3o1r\|3o1r]], [[3o1t\|3o1t]], [[3o1u\|3o1u]], [[3o1v\|3o1v]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alkB, aidD, b2212, JW2200 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alkB, aidD, b2212, JW2200 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3o1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o1s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3o1s RCSB], [http://www.ebi.ac.uk/pdbsum/3o1s PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3o1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o1s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3o1s RCSB], [http://www.ebi.ac.uk/pdbsum/3o1s PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ALKB_ECOLI ALKB_ECOLI]] Dioxygenase that repairs alkylated DNA and RNA containing 3-methylcytosine or 1-methyladenine by oxidative demethylation. Has highest activity towards 3-methylcytosine. Has lower activity towards alkylated DNA containing ethenoadenine, and no detectable activity towards 1-methylguanine or 3-methylthymine. Accepts double-stranded and single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron. Provides extensive resistance to alkylating agents such as MMS and DMS (SN2 agents), but not to MMNG and MNU (SN1 agents).<ref>PMID:12226668</ref> <ref>PMID:12594517</ref> <ref>PMID:16482161</ref> <ref>PMID:19706517</ref> <ref>PMID:21068844</ref> <ref>PMID:20084272</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 17:
	Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase.,Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X, Yang CG, Cui Q, He C Nature. 2010 Nov 11;468(7321):330-3. PMID:21068844<ref>PMID:21068844</ref>		Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase.,Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X, Yang CG, Cui Q, He C Nature. 2010 Nov 11;468(7321):330-3. PMID:21068844<ref>PMID:21068844</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 22:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
-	[[Category: Cui, Q.]]	+	[[Category: Cui, Q]]
-	[[Category: Dai, Q.]]	+	[[Category: Dai, Q]]
-	[[Category: He, C.]]	+	[[Category: He, C]]
-	[[Category: Hou, G.]]	+	[[Category: Hou, G]]
-	[[Category: Jia, G.]]	+	[[Category: Jia, G]]
-	[[Category: Jian, X.]]	+	[[Category: Jian, X]]
-	[[Category: Yang, C G.]]	+	[[Category: Yang, C G]]
-	[[Category: Yi, C.]]	+	[[Category: Yi, C]]
-	[[Category: Zhang, W.]]	+	[[Category: Zhang, W]]
-	[[Category: Zheng, G.]]	+	[[Category: Zheng, G]]
	[[Category: Demethylase]]		[[Category: Demethylase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 07:16, 28 May 2014

2014-05-28T07:16:01Z

←Older revision		Revision as of 07:16, 28 May 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3o1s\| PDB=3o1s \| SCENE= }}~~	+	==Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase==
-	===Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase===	+	<StructureSection load='3o1s' size='340' side='right' caption='[[3o1s]], [[Resolution\|resolution]] 1.58Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21068844}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3o1s]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O1S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3O1S FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2YR:2-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>2YR</scene>, <scene name='pdbligand=MDQ:2-DEOXY-3-(OXIDOMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>MDQ</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3o1m\|3o1m]], [[3o1o\|3o1o]], [[3o1p\|3o1p]], [[3o1r\|3o1r]], [[3o1t\|3o1t]], [[3o1u\|3o1u]], [[3o1v\|3o1v]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alkB, aidD, b2212, JW2200 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3o1s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o1s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3o1s RCSB], [http://www.ebi.ac.uk/pdbsum/3o1s PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mononuclear iron-containing oxygenases conduct a diverse variety of oxidation functions in biology, including the oxidative demethylation of methylated nucleic acids and histones. Escherichia coli AlkB is the first such enzyme that was discovered to repair methylated nucleic acids, which are otherwise cytotoxic and/or mutagenic. AlkB human homologues are known to play pivotal roles in various processes. Here we present structural characterization of oxidation intermediates for these demethylases. Using a chemical cross-linking strategy, complexes of AlkB-double stranded DNA (dsDNA) containing 1,N(6)-etheno adenine (epsilonA), N(3)-methyl thymine (3-meT) and N(3)-methyl cytosine (3-meC) are stabilized and crystallized, respectively. Exposing these crystals, grown under anaerobic conditions containing iron(II) and alpha-ketoglutarate (alphaKG), to dioxygen initiates oxidation in crystallo. Glycol (from epsilonA) and hemiaminal (from 3-meT) intermediates are captured; a zwitterionic intermediate (from 3-meC) is also proposed, based on crystallographic observations and computational analysis. The observation of these unprecedented intermediates provides direct support for the oxidative demethylation mechanism for these demethylases. This study also depicts a general mechanistic view of how a methyl group is oxidatively removed from different biological substrates.

-	~~==Function==~~	+	Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase.,Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X, Yang CG, Cui Q, He C Nature. 2010 Nov 11;468(7321):330-3. PMID:21068844<ref>PMID:21068844</ref>
-	~~[[http://www.uniprot.org/uniprot/ALKB_ECOLI ALKB_ECOLI]] Dioxygenase that repairs alkylated DNA and RNA containing 3~~-~~methylcytosine or 1-methyladenine by oxidative demethylation. Has highest activity towards 3-methylcytosine. Has lower activity towards alkylated~~ DNA ~~containing ethenoadenine, and no detectable activity towards 1-methylguanine or 3-methylthymine. Accepts double-stranded and single-stranded substrates~~. ~~Requires molecular oxygen~~, ~~alpha-ketoglutarate and iron~~. ~~Provides extensive resistance to alkylating agents such as MMS and DMS~~ (~~SN2 agents), but not to MMNG and MNU (SN1 agents~~).~~<ref>~~PMID:~~12226668</ref> <ref>PMID:12594517</ref> <ref>PMID:16482161</ref> <ref>PMID:19706517</ref>~~ <ref>PMID:21068844</ref> ~~<ref>PMID:20084272</ref>~~	+

-	~~==About this Structure==~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3o1s]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3O1S OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:021068844</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
-	[[Category: ~~Escherichia coli k-12~~]]	+	</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Cui, Q.]]		[[Category: Cui, Q.]]
	[[Category: Dai, Q.]]		[[Category: Dai, Q.]]

OCA at 08:50, 19 June 2013

2013-06-19T08:50:31Z

←Older revision		Revision as of 08:50, 19 June 2013
Line 1:		Line 1:
	{{STRUCTURE_3o1s\| PDB=3o1s \| SCENE= }}		{{STRUCTURE_3o1s\| PDB=3o1s \| SCENE= }}
	===Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase===		===Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase===
-	{{~~ABSTRACT_PUBMED_021068844~~}}	+	{{ABSTRACT_PUBMED_21068844}}

	==Function==		==Function==
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[3o1s]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli~~ Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O1S OCA].	+	[[3o1s]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O1S OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:021068844</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:021068844</ref><references group="xtra"/><references/>
-	[[Category: Escherichia coli]]	+	[[Category: Escherichia coli k-12]]
	[[Category: Cui, Q.]]		[[Category: Cui, Q.]]
	[[Category: Dai, Q.]]		[[Category: Dai, Q.]]

OCA: Protected "3o1s" [edit=sysop:move=sysop]

2013-04-24T11:53:15Z

Protected "3o1s" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:53, 24 April 2013

OCA at 11:53, 24 April 2013

2013-04-24T11:53:12Z

←Older revision		Revision as of 11:53, 24 April 2013
Line 1:		Line 1:
-	{{Seed}}
-	[[Image:3o1s.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3o1s", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3o1s\| PDB=3o1s \| SCENE= }}		{{STRUCTURE_3o1s\| PDB=3o1s \| SCENE= }}
-
	===Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase===		===Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase===
		+	{{ABSTRACT_PUBMED_021068844}}

		+	==Function==
		+	[[http://www.uniprot.org/uniprot/ALKB_ECOLI ALKB_ECOLI]] Dioxygenase that repairs alkylated DNA and RNA containing 3-methylcytosine or 1-methyladenine by oxidative demethylation. Has highest activity towards 3-methylcytosine. Has lower activity towards alkylated DNA containing ethenoadenine, and no detectable activity towards 1-methylguanine or 3-methylthymine. Accepts double-stranded and single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron. Provides extensive resistance to alkylating agents such as MMS and DMS (SN2 agents), but not to MMNG and MNU (SN1 agents).<ref>PMID:12226668</ref> <ref>PMID:12594517</ref> <ref>PMID:16482161</ref> <ref>PMID:19706517</ref> <ref>PMID:21068844</ref> <ref>PMID:20084272</ref>

	==About this Structure==		==About this Structure==
-	~~3O1S~~ is a 3 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O1S OCA].	+	[[3o1s]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O1S OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021068844</ref><references group="xtra"/><references/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Cui, Q.]]		[[Category: Cui, Q.]]
Line 28:		Line 24:
	[[Category: Demethylase]]		[[Category: Demethylase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Nov 18 00:52:05 2010''

OCA at 21:40, 17 November 2010

2010-11-17T21:40:51Z

←Older revision		Revision as of 21:40, 17 November 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3o1s.jpg\|left\|200px]]

-	The ~~entry 3o1s~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3o1s", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3o1s\| PDB=3o1s \| SCENE= }}

-	~~Authors: Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.~~-~~G., Cui, Q., He, C.~~	+	===Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase===

-	Description: Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Aug~~ 18 11:24:14 2010''	+	==About this Structure==
		+	3O1S is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O1S OCA].
		+	[[Category: Escherichia coli]]
		+	[[Category: Cui, Q.]]
		+	[[Category: Dai, Q.]]
		+	[[Category: He, C.]]
		+	[[Category: Hou, G.]]
		+	[[Category: Jia, G.]]
		+	[[Category: Jian, X.]]
		+	[[Category: Yang, C G.]]
		+	[[Category: Yi, C.]]
		+	[[Category: Zhang, W.]]
		+	[[Category: Zheng, G.]]
		+	[[Category: Demethylase]]
		+	[[Category: Oxidoreductase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Nov 18 00:52:05 2010''

OCA at 07:16, 18 August 2010

2010-08-18T07:16:41Z

←Older revision		Revision as of 07:16, 18 August 2010
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3o1s is ON HOLD	+	The entry 3o1s is ON HOLD until Paper Publication

-	Authors: Yi, C., Jia, G., Hou, G., Dai, ~~Qing~~, Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.	+	Authors: Yi, C., Jia, G., Hou, G., Dai, Q., Zhang, W., Zheng, G., Jian, X., Yang, C.-G., Cui, Q., He, C.

	Description: Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase		Description: Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug ~~4 08~~:51:36 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 18 11:24:14 2010''